Had Root Canal + 2nd Root Canal + Apicoectomy & Still Pain!

I had a root canal done by an endodontist on my #14 (1st molar upper left) about 6 months ago, then later a 2nd root canal (re-treatment) and then finally an apicoectomy (about 2 months ago) and I still have pain! That tooth is no longer sensitive to touch like it was before the apicoectomy but I still have pain that comes and gos and that radiates to my ear and jaw. I think I might have TMJ because my left jaw pops and clicks when I open my mouth wide or when I eat. At first I thought that I'm having TMJ because I used to wear braces but stopped wearing my retainer and that my teeth are shifting and causing problems, but my orthodontist said that my teeth have not moved that much. So the only other explanation could be the fact that I've been eating only on my right side for many months and thats why I'm now having a TMJ problem. My left jaw hurts and have a severe earache (left), but I also feel like the pain is coming from that tooth, Why? Can it possibly still be infected or is it inflammation?